› 1zxz

X-ray diffraction
2.8Å resolution

X-ray structure of peptide deformylase from Arabidopsis thaliana (AtPDF1A); crystals grown in PEG-5000 MME as precipitant

Released:
DOI: 10.2210/pdb1zxz/pdb
PDB entry 1zxz coloured by chain, front view.
PDB entry 1zxz coloured by chain, side view.
PDB entry 1zxz coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms.
Fieulaine S, Juillan-Binard C, Serero A, Dardel F, Giglione C, Meinnel T, Ferrer JL
J Biol Chem 280 42315-24 (2005)
PMID: 16192279

Function and Biology Details

Reaction catalysed: 
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190375 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase 1A, chloroplastic/mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 197 amino acids
Theoretical weight: 22.31 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9FV53 (Residues: 78-267; Coverage: 71%)
Gene names: At1g15390, DEF1, F9L1.34, F9L1_34, PDF1A
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P212121
Unit cell:
a: 51.2Å b: 73.8Å c: 109.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.236 0.291
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Metalloproteomics, metalloproteomes, and the annotation of metalloproteins.
Maret W. (2010)
4 more

1 mention without citation

Structure and activity of human mitochondrial peptide deformylase, a novel cancer target.
Escobar-Alvarez et al. (2009)